Yesterday I received a semi-spam e-mail from Royal Society Publishing, publisher of Biology Letters and Philosophical Transactions, saying that all of their articles that are more than 70 years old are now freely accessible. In itself, this is a laudable move, of course. And you could say it's an important step in the more general shift towards an open access model of academic publishing (i.e., a model were all academic papers are freely accessible for everyone). But I couldn't help being a little skeptical, particularly after having read this note, attached to a torrent, which I came across a few months back (a torrent is a file that serves as a 'handle' for downloading more and larger files). The Pirate Bay is not a place were you would normally expect to encounter political statements, but this torrent of 18,592 papers, all published prior to 1923, from the archive of the Philosophical Transactions is accompanied by a text that conveys many of the same frustrations that I feel when it comes to academic publishing.

First, the uploader (who calls himself Greg Maxwell, which kind of sounds like a real name) explains that the part of the archive that the Royal Society has so valiantly decided to make freely available, was largely, if not entirely in the public domain to begin with. Copyright simply expires after some time. As the uploader writes (this was before the Royal Society opened up their archive):

"The documents are part of the shared heritage …

PLoS Biology celebrates the release of Paul Feyerabend's latest book, The Tyranny of Science, with two book reviews. (The Tyranny of Science was published posthumously, as Feyerabend passed away in 1994.) Before we get to the reviews, let's start with some quotes from Feyerabend's 1975 claim-to-fame bestseller, Against Method, to give you a flavor of what the famous philosopher of science was all about (no quotes from The Tyranny, I'm afraid, because I don't have a copy):

"Science is an essentially anarchistic enterprise. (...) The only principle that does not inhibit progress is: anything goes."

What a delightful opening! Although I would have expected no less from a celebrity intellectual from the 70s. Perhaps the statement is a bit devoid of meaning, but it makes very clear that, in Against Method, shit is going to hit the fan. (Incidentally, I assure you that our department, with its 12:30 brown-bag lunches, departmental Christmas dinners, yearly outings, and weekly drinks on Friday at 5, is far removed from an anarchist stronghold.)

Feyerabend continues:

"For example, we may use hypotheses that contradict well-confirmed theories (...)."

Sure, a little controversy is always good.

"No theory ever agrees with all the facts in its domain, yet it is not always the theory that is to blame."

Well, ok, I suppose. I would say that, if something is refuted, it was never really a fact to begin with. But that's largely semantics, because it's no trivial matter to distinguish facts from hypotheses. So in practice he's right …

I wrote a guest post about OpenSesame on the NeuroDebian 'insider blog' (link), and I thought this would be a good time to share how development of OpenSesame 0.25 "Dashy Darwin" is coming along.

And "Dashy Darwin" is coming along nicely! A lot of bugs have already been fixed. There's not much new functionality, but quite a bit of polish has been added to the interface. For example, the controls of the sequence item have been revamped (see the screenshot above). You can now re-order and add new items to a sequence by dragging and dropping, which is a definite improvement over the use of buttons.

For those who are keen to try out the new version, experimental packages (0.25-pre1, Windows, Linux and Source — no Mac OS yet, sorry!) can be downloaded here. But the usual warnings apply: This is a potentially highly unstable, experimental snapshot!

We all know shortcuts like this:

Photo: Jan-Dirk van der Burg (olifantenpaadjes.nl)

Trails of this sort go by various names. In a photo album devoted entirely to the subject, the Dutch photographer Jan-Dirk van der Burg has coined (or at least popularized) the term "elephant trail" (olifantenpaadje). Wikipedia adopts the more sensuous "desire path". And, of course, there is the simple "shortcut". But regardless the name, it is an intriguing phenomenon. Because these trails are shortcuts, to be sure, but usually not quite the shortest path.

Photo: Jan-Dirk van der Burg (olifantenpaadjes.nl)

But why? If you're going to leave the sidewalk anyway, why not head straight to wherever you need to go? Why the little curve, the minor inefficiency? Surely not to please the likes of van der Burg, who revel in their shape and form.

Photo: Jan-Dirk van der Burg (olifantenpaadjes.nl)

Surprisingly enough, desire paths can be modeled fairly easily. Helding and colleagues have proposed a model in which they are the result of only two opposing "social forces": The tendency to take the shortest path (i.e., a straight line) and the tendency to take the most comfortable path.

The crux of the model is the assumption that paths become increasingly more comfortable as people use them. Which is true, of course, because usage smoothens a path by killing off vegetation, etc. Another factor is the social comfort of walking where others have walked before: Most people do not want to be a rogue wanderer …

Right now I'm reading Philip Ball's trilogy on "nature's patterns". In three books (Shapes, Flow and Branches), Ball describes all kinds of patterns, from the black and white stripes on a zebra's coat to the shape of a milk splash. These are quite possibly the best (not too) popular science books that I've read in years, but more about that some other time, perhaps. Right now I want to focus on one thing that I found particularly intriguing: Ball's description of the organized motion of a swarm.

By definition, a swarm consists of a group of individuals. In the case of bees, and arguably in the case of humans as well, these individuals are driven by simple impulses. They react to other individuals in their immediate vicinity, but there is no master plan, and very little in the way of group coordination. And yet, somehow, from this teeming, chaotic mess, organized behavior does arise.

Consider, for example, what happens when a few bees have discovered a potential nest site, or some other place-to-bee. You might expect the few "informed" bees to separate from the swarm, being unable to communicate their find and thus unable to convince the other members of the swarm to follow their lead. Or you might expect the informed bees to be re-absorbed into the chaos of the swarm, quickly forgetting their find. But, surprisingly enough, this doesn't need to happen: A few informed bees can cause an entire swarm to migrate towards a newly discovered …